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He añadido al visor de muestras el plot de IC.

main
marcelcosta 2 years ago
parent
commit
20bf1d2c20
1 changed files with 32 additions and 2 deletions
  1. +32
    -2
      BDAccess/app.R

+ 32
- 2
BDAccess/app.R

@ -77,7 +77,7 @@ ui <- fluidPage(
htmlOutput("report"),
h3("Nitrogen"),
tableOutput("nitrogen"),
plotOutput("visorplot")
plotOutput("visorplot", height = "1000px")
)
),
@ -831,7 +831,7 @@ server <- function(input, output) {
if (input$nhc == 3){
pops<-sqlFetch(dta, "POPULATIONS")
pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
"CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
ggplot(aes(pop, value))+
@ -839,6 +839,36 @@ server <- function(input, output) {
labs(title = input$id, y="% parent", x="")+
theme_bw()+
theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5))
tl<-sqlFetch(dta, "IC") %>% filter(samples == input$id)
mtl<-melt(tl, variable.name = "Receptors")
mtl$Receptors<-as.character(mtl$Receptors) #Para poder depurar bien el texto, lo pasamos a tipo character
mtl$Receptors<-gsub("n","-",mtl$Receptors, fixed = T)
mtl$Receptors<-gsub("p","+",mtl$Receptors, fixed = T)
mtl$Receptors<-gsub("_"," ",mtl$Receptors)
mtl[mtl$value < 1, "Receptors"]<-"Other"
mtl$Receptors<-gsub("[A-Z]*-*[0-9T]- *", "", mtl$Receptors)
mtl$Receptors<-gsub("+ $", "", mtl$Receptors)
mtl$Receptors[mtl$Receptors == ""]<-"All Negative"
mtl$Receptors<-factor(mtl$Receptors)
mtl$Population<-factor(mtl$Population, levels = c("CD8", "CD4"))
# colorCount<-length(unique(mtl$Receptors))
# getPalette = colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))
color<-c(c("CTLA4+ LAG3+ PD1+ TIGIT+ TIM3+"="black","All Negative"="white","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E","TIGIT+"="#FA7055"),
c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F","PD1+ TIGIT+"="#D259AA", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "CTLA4+ TIGIT+"="#9C929A", "LAG3+ TIM3+"="#9ED848", "TIGIT+ TIM3+"="#ACB353", "LAG3+ TIGIT+"="#EC964A"),
c("CTLA4+ PD1+ TIGIT+"="#B86B6A","CTLA4+ PD1+ TIGIT+ TIM3+"="#B81515","LAG3+ PD1+ TIGIT+"="#007D8A", "PD1+ TIGIT+ TIM3+"="#D64545", "LAG3+ PD1+ TIGIT+ TIM3+"="#0f5860", "LAG3+ TIGIT+ TIM3+"="#50cad3"))
g_IC<-ggplot(mtl, aes(samples, value, fill=Receptors))+
geom_bar(stat="summary", fun="sum",color="black")+
labs(x="Patient", y="% CD8+", fill="")+
facet_grid(.~Population)+
scale_fill_manual(values = color[levels(mtl$Receptors)[levels(mtl$Receptors) %in% unique(mtl$Receptors)]])+
theme_bw()+
theme(axis.text.x=element_text(angle=45, hjust=1))
ggpubr::ggarrange(g_pop, g_IC, heights = c(0.4, 0.6), ncol = 1)
}
})

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